Genomics Phase 2 Digital Initiative

A central goal of biological research is to understand the functional map between the static genetic makeup of an individual (the genome) through the dynamic intermediate molecular states (including the transcriptome and proteome) to their observable characteristics (the phenome), such as disease state, grain yield or fibre quality. Consequentially novel technologies that can accurately and rapidly map these ‘omics processes have broad applicability across many domains including Agriculture, Health and the Environment.

The Genomics Initiative’s goal is to advance genomics and ‘omics science to enable the delivery of optimal technologies for the benefit of new and existing Australian industry with an initial focus on food security and agricultural productivity. This goal aligns with the Federal Government’s Science and Research Food Priority to enhance food and fibre production and the goal of the National Farmers’ Federation and Federal Government to grow the Australian agricultural sector to AU$100B by 2030. These explicitly focus on achieving their aims through the development of practical and novel technologies that will accelerate productivity and efficiency gains for Australian agriculture producers. Genomics and ‘omics technologies can play a key role in maximising the efficacy, diversity, biosecurity and yield of agricultural species under changing and challenging conditions.
The pilot study phase of the Genomics Initiative using wheat as a test case was successfully completed in April 2020. The pilot delivered a prototype artificial intelligence (AI) platform for phenomics data collection using low cost sensors and advanced foundational graph research enabling the capture of all the genomic variation within populations of species with complex genomes such as wheat.

This next phase proposes to build upon the pilot outputs to create two new ‘omics software platforms. The Pan ‘omics Toolbox work package will be a single cohesive platform formed through the creation of solutions for the optimal representation, integration and annotation, querying and translation of population scale ‘omics data. This will enable industry and researchers to expedite the identification of novel ‘omics targets and management strategies across the agricultural, health or environmental domains. The Video Phenomics work package will continue the development of the prototype AI platform for the automatic capture, quantification and prediction of traits enabling the accurate capture of phenomics data using low cost sensors and through the utilisation of augmented reality. This will significantly broaden the accessibility and scalability of phenomics technology.

The two platforms used jointly will further accelerate the discovery of new knowledge to inform biological system interventions such as gene editing and breeding selection of any species. For instance, by combining accurate wheat spike count data collected via the Video Phenomics platform with wheat ‘omic data integrated using the Pan ‘omics Toolbox, the toolbox will then be able to predict which set of genes could be targeted via gene editing to improve wheat yield leading to improved agricultural productivity for Australia.

The initiative has strong industry engagement through InterGrain, a leading private Australian cereal breeding company, providing access to their internal phenomics trials, provision of data, equipment and personnel. This initiative is a close collaboration between CSIRO’s Data61 and Agriculture and Food Business Units, leveraging existing research, expertise and engagements from both.

The Genomics Initiative will drive forward the development of sustainable and alternative protein products and industries by delivering technologies to enable, enhance and accelerate research undertaken in the Future Protein CSIRO Mission. The Genomics Initiative will enable population-scale ‘omics to be used successfully in the Future Protein Mission to increase the diversity of healthy, sustainably-produced protein in the global food ecosystem by 30% by 2030 and more broadly for the advantage of agriculture, industry and society.